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Monday, February 2, 2015

Startup bioinformatics firm Reference Genomics has won the US Centers for Disease Control and Prevention's $200,000 "No-Petri-Dish" Challenge, the company said on Monday.

The challenge called for contestants to develop a rapid "straight-to-strain" method for identifying Shiga toxin-producing E. coli, a common cause of severe foodborne outbreaks. Using next-generation sequencing data, Reference Genomics' method provides fast, high-resolution diagnostics results and can be used for metagenomic samples with "extremely low concentrations of E. coli or other pathogens," it said.

Current methods of detecting STEC include culture-based approaches, which can take days or weeks to get results, and PCR-based tests, which can provide results more quickly but are less informative, said Reference Genomics, which also goes by the name of its platform called One Codex.

"The developers of One Codex succeeded in demonstrating how their platform can rapidly identify STEC from complex clinical samples and provide meaningful information about its strain-type and characteristics, even when the pathogens are present at levels too low to support assembly-based methods," CDC said in a statement. The "No-Petri-Dish Challenge is part of the center's Advanced Molecular Detection initiative.

The One Codex platform is currently in beta mode, and San Francisco-based Reference Genomics is "building the largest index of genomic data and better search algorithms for fast, accurate bacterial and viral identification," it said.